Description of the Related Art
The antibiotic chlortetracycline and its derivative compounds (e.g., tetracycline, demethylchlortetracycline, demethyltetracycline) are produced commercially in submerged fermentation by Streptomyces aureofaciens (Dugar, 1948). More than thirty years of industrial manipulation of this microorganism has resulted in the development of sophisticated fermentation techniques and media formulations that have allowed significant improvements in fermentation yield (Goodman, 1985). These advances in yield improvement have also been aided by the isolation of mutants of S. aureofaciens with increased ability to produce antibiotic (Veselova, 1969). These high-producing strains have largely been isolated by the process of mutagenesis, followed by random screening for improved yield. The same techniques allowed the isolation of mutants blocked in antibiotic biosynthesis which were critical tools for the elucidation of the biosynthetic sequence for chlortetracycline formation (McCormick, 1968). Despite these accomplishments, an understanding of the genetic regulation of chlortetracycline biosynthesis was not completely realized. Recent developments in the field of Streptomyces genetics have created the opportunity to study molecular genetics of organisms producing industrially important metabolites.
The demonstration of recombination of chromosomal markers by the fusion and subsequent regeneration of Streptomyces protoplasts (Hopwood et al., 1978 and Baltz et al., 1981) was a pivotal event in the genetics of the actinomycetes. Prior to the development of techniques for protoplast fusion, genetic crosses could only be reliably performed in a few species with demonstrated conjugal systems (Hopwood, 1967). Now, genetic analysis can be performed in any species which can be protoplasted and regenerated. More importantly, protoplasts later proved to be an ideal substrate for transformation by plasmid DNA, thus creating the opportunity to do recombinant DNA experiments in these organisms (Bibb et al., 1978). The isolation of genes for several antibiotic resistances, such as thiostrepton, viomycin and neomycin, allowed the construction of readily selectable cloning vectors from indigenous Streptomyces plasmids (Thompson et al., 1982).
One of the first antibiotic biosynthetic genes to be cloned was the O-methyltransferase involved in the formation of the antibiotic pigment undecylprodigiosin (UDP) (Feitelson et al., 1980). The gene was identified by its ability to complement a known mutation in the UDP biosynthetic pathway. Other techniques employed in these early efforts to isolate biosynthetic genes included mutational cloning using phage OC31 for methylenomycin (Chater et al., 1983), a sib selection of recombinant clones using in vitro enzyme assays for the actinomycin phenoxa-zinone synthetase (Jones et al., 1984) and sulphonamide resistance conferred by the p-aminobenzoic acid synthetase involved in candicidin production (Gil et al., 1983). Bialaphos biosynthetic genes were identified via complementation of blocked mutants (Murakami et al., 1986).
Genes involved in actinorhodin biosynthesis were cloned by complementation of biosynthetically blocked mutants of Streptomyces coelicolor (Malpartida et al., 1984). In this last case, two overlapping clones complementing distinct classes of mutants were combined on a single plasmid which was shown to confer the ability to synthesize actinorhodin when introduced into a heterologous Streptomyces parvulus host.
Another important series of observations was that genes for antibiotic biosynthesis were physically linked to the resistance determinant(s) for that same antibiotic in the producing organism. Thus, a DNA fragment from Streptomyces griseus conferring streptomycin resistance was shown to be contiguous with DNA that complemented biosynthetic blocks (Distler et al., 1985). The same situation was seen in Streptomyces fradiae where biosynthetic genes had been identified by probing a cosmid library for homology to a mixed-base oligonucleotide constructed to represent the DNA sequence for the aminoterminus of the final enzyme in the tylosin biosynthetic pathway (Fishman et al., 1989). A previously cloned tylosin resistance gene (tlrB) was shown to be contained within this region of DNA, which complemented nine classes of blocked mutants (Baltz et al., 1988). In the cases of puromycin (Vara et al., 1988) and tetracenomycin (Motamedi et al., 1987), a primary selection for expression of antibiotic resistance gene in the heterologous host Streptomyces lividans allowed subsequent identification of antibiotic biosynthetic genes located on the same cloned DNA fragment.
The use of nucleic acid probes has aided the isolation of biosynthetic genes. This approach relies on the existence of a pre-existing body of information concerning the pathway or prior cloning having been performed. Thus, in the case of tylosin above, a probe was constructed using information from a partial amino acid sequence of a biosynthetic enzyme (Fishman et al., 1987). Similarly, the gene for isopenicillin N synthetase was cloned from Streptomyces clavuligerus by identifying a clone hybridizing to an oligonucleotide probe constructed with a knowledge of the N-terminal amino acid sequence of the enzyme (Leskiw, 1988). Genes involved in the biosynthesis of erythromycin were identified by probing a cosmid library with a previously cloned erythromycin resistance gene (Stanzak, 1986). Similarly, genes involved in the biosynthesis of oxytetracycline have been identified by hybridization to both a previously cloned resistance determinant (Butler et al., 1989) and an oligonucleotide synthesized to represent the DNA sequence corresponding to the partially elucidated amino acid sequence of the biosynthetic enzyme anhydrotetracycline oxygenase (Binnie et al., 1989). The use of heterologous actI and actIII probes allowed the identification of genes involved in anthracycline biosynthesis in Streptomyces peucetius (Stutzman-Engwall et al., 1989).
The use of these techniques individually or in combination has allowed the isolation or assembly of entire biosynthetic pathways from fragments of genes, and in some instances, their expression in a heterologous host. The entire biosynthetic cluster for bialaphos was cloned by a combination of selections for complementing activities and heterologous expression of bialaphos resistance (Murakami et al., 1986). While a successful isolation of the entire pathway in a single step in Streptomyces lividans by selecting for bialaphos resistance was noted, no mention is made concerning expression of the biosynthetic genes.
A bifunctional cosmid clone which hybridized to a homologously derived erythromycin resistance determinant was isolated from a Saccharopolyspora erythrea library and shown to direct the synthesis of erythromycin when transferred to Streptomyces lividans (Stanzak et al., 1986). An E. coli cosmid clone that showed hybridization to both an oxytetracycline resistance gene probe and biosynthetic gene probe (for anhydrotetracycline oxygenase) allowed the isolation of the oxytetracycline biosynthetic cluster from Streptomyces rimosus (Binnie et al., 1989). Subsequent subcloning into a Streptomyces plasmid vector allowed production of oxytetracycline in Streptomyces lividans.
Two overlapping clones from the tetracenomycin producer were identified by complementation of blocked mutants of Streptomyces glaucescens and ability to confer tetracenomycin resistance in S. lividans (Motamedi et al., 1987). When both were separately resident in S. lividans and co-fermented, or when they were co-resident in the same S. lividans host, tetracenomycin was produced. Bifunctional clones isolated from an E. coli library of Streptomyces peucetius DNA by hybridization to actI and actIII probes of S. coelicolor were shown to direct the synthesis of pigmented antibiotic when introduced into S. lividans (Stutzman-Engwall, 1989).
Additionally, the isolation of the biosynthetic pathway for cepthamycin C production has occurred (Chen et al., 1988). In this case, random clones in S. lividans were individually screened for cephamycin C production using an agar plug fermentation method. Out of 30,000 screened, one transformant of S. lividans was shown to be producing cephamycin C.
Although reports have been published concerning the cloning of a tetracycline-resistance determinant (Reynes et al., 1988) and a bromoperoxidase (Van Pee, 1988) from Streptomyces aureofaciens, these studies are in no way extended toward the isolation of chlortetracycline biosynthetic genes or the entire gene cluster.
The present invention is the first instance wherein the single DNA gene cluster related to the entire biosynthetic pathway for producing tetracycline and chlortetracycline is isolated and utilized.